Circular RNA profiling of the rice photo-thermosensitive genic male sterile line Wuxiang S reveals circRNA involved in the fertility transition

Liu

Zhu

et al. 2020

IJMS

Circular RNAs (circRNAs) are endogenous noncoding RNAs with covalently closed continuous loop structures that are formed by 3 -5 ligation during splicing. These molecules are involved in diverse physiological and developmental processes in eukaryotic cells. Jasmonic acid (JA) is a critical hormonal regulator of plant growth and defense. However, the roles of circRNAs in the JA regulatory network are unclear. In this study, we performed high-throughput sequencing of Arabidopsis thaliana at 24 h, 48 h, and 96 h after methyl JA (MeJA) treatment. A total of 8588 circRNAs, which were distributed on almost all chromosomes, were identified, and the majority of circRNAs had lengths between 200 and 800 bp. We identified 385 differentially expressed circRNAs (DEcircRNAs) by comparing data between MeJA-treated and untreated samples. Gene Ontology (GO) enrichment analysis of the host genes that produced the DEcircRNAs showed that the DEcircRNAs are mainly involved in response to stimulation and metabolism. Additionally, some DEcircRNAs were predicted to act as miRNA decoys. Eight DEcircRNAs were validated by qRT-PCR with divergent primers, and the junction sites of five DEcircRNAs were validated by PCR analysis and Sanger sequencing. Our results provide insight into the potential roles of circRNAs in the MeJA regulation network.

Section: Discussionsupporting

confidence: 91%

Identification and Characterization of circRNAs Responsive to Methyl Jasmonate in Arabidopsis thaliana

Liu

Zhu

et al. 2020

IJMS

“…Our previous studies showed that the fertility transition of WXS is controlled by photoperiod and temperature: it was completely male sterile when grown under the high temperatures (≥23.5°C) and long-day (≥14 h) conditions; in contrast, it becomes fertile under the conditions of low temperature (approximately 21°C) and short day length (12 h) during anthers development. Study of cytological observation indicated that abortion starts from the stage of pollen mother cells (PMCs) formation and throughout the reproductive process ( Zhang et al, 2016 ; Wang et al, 2019 ). Therefore, WXS is an ideal experimental system in which to identify lncRNAs that act during the fertility transition.…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Identification of lncRNAs Involved in Fertility Transition in the Photo-Thermosensitive Genic Male Sterile Rice Line Wuxiang S

Wang

et al. 2021

Front. Plant Sci.

Self Cite

Long non-coding RNAs (lncRNAs) act as universal regulators of various biological processes, but no genome-wide screening of lncRNAs involved in the fertility transition of the photo-thermosensitive genic male sterile (PTGMS) rice line has been reported. Here, we performed strand-specific RNA sequencing at three developmental stages of a novel PTGMS line Wuxiang S (WXS). A total of 3,948 lncRNAs were identified; 622 of these were detected as differentially expressed lncRNAs (DE-lncRNAs) between male-sterile WXS (WXS-S) and male-fertile WXS (WXS-F). A large proportion of lncRNAs differentially expressed at the stage of pollen mother cells meiosis, suggested that it may be the most critical stage for fertility transition of WXS. Furthermore, functional annotation of the cis- and trans- targets of DE-lncRNAs showed that 150 targets corresponding to 141 DE-lncRNAs were identified as involved in anther and pollen development. Moreover, computational analysis predicted 97 lncRNAs as precursors for 72 miRNAs, and 94 DE-lncRNAs as potential endogenous target mimics (eTMs) for 150 miRNAs. Finally, using the dual luciferase reporter assays, we demonstrated that two lncRNAs act as eTMs to regulate the expression of the SPL and GRF genes by competing for the shared osa-miR156 and osa-miR396, respectively. These genomic characteristics, differential expression, and interaction of lncRNAs with miRNAs and mRNAs contribute to our understanding of the roles of lncRNAs during the fertility transition in PTGMS rice lines.

“…Table S2). The number of circRNAs identified in this study was larger than that in leaf development of tea (558) (Tong et al 2018 ), in leaf and root of cucumber under salt stress (2787) (Zhu et al 2019 ), in roots, stems, leaves, flowers and siliques of Arabidopsis across the lifespan (5861) (Chen et al 2017b ), in maize leaf under different stress treatment (1199) (Han et al 2020 ), in wheat leaves in the dehydration stress response (88) (Wang et al 2017b ), in potato stem tissues in response to Pectobacterium carotovorum subspecies brasiliense infection (2098) (Zhou et al 2018 ), and in tomato during fruit ripening process (705) (Yin et al 2018 ), but less than that in fertility transition of rice photo-thermosensitive genic male sterile line (9994) (Wang et al 2019 ). The reason for the number difference of identified circRNAs may be attributed to the difference of sample type and number, and most probably to the variety of plant species.…”

Section: Discussionmentioning

confidence: 99%

“…After quality confirmation of the total RNAs, the library construction for circRNAs was performed according to the protocol as previously described (Tong et al 2018 ; Wang et al 2019 ). Briefly, a total of 2.0 μg RNA per qualified sample was performed to remove ribosomal RNA using the Ribo-Zero rRNA Removal Kit (Epicentre, Madison, WI, USA).…”

Section: Methodsmentioning

confidence: 99%

“…Besides, a total of 705 circRNAs were detected in mature green tomato fruit and red ripening ones, of which 340 circRNAs were differentially expressed to involve in fruit ripening process (Yin et al 2018 ). A total of 9994 circRNAs were obtained in young panicles of WXS rice at three development stages, of which 186 circRNAs were significantly differentially expressed to participate in fertility transition process (Wang et al 2019 ). Some studies have reported the functional researches of circRNAs in plants.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Systematic identification and characterization of circular RNAs involved in flag leaf senescence of rice

Huang

Guo

et al. 2021

Planta

Main conclusion Circular RNAs (circRNAs) identification, expression profiles, and construction of circRNA-parental gene relationships and circRNA-miRNA-mRNA ceRNA networks indicate that circRNAs are involved in flag leaf senescence of rice. Abstract Circular RNAs (circRNAs) are a class of 3′-5′ head-to-tail covalently closed non-coding RNAs which have been proved to play important roles in various biological processes. However, no systematic identification of circRNAs associated with leaf senescence in rice has been studied. In this study, a genome-wide high-throughput sequencing analysis was performed using rice flag leaves developing from normal to senescence. Here, a total of 6612 circRNAs were identified, among which, 113 circRNAs were differentially expressed (DE) during the leaf senescence process. Moreover, 4601 (69.59%) circRNAs were derived from the exons or introns of their parental genes, while 2110 (71%) of the parental genes produced only one circRNA. The sequence alignment analysis showed that hundreds of rice circRNAs were conserved among different plant species. Gene Ontology (GO) enrichment analysis revealed that parental genes of DE circRNAs were enriched in many biological processes closely related to leaf senescence. Through weighted gene co-expression network analysis (WGCNA), six continuously down-expressed circRNAs, 18 continuously up-expressed circRNAs and 15 turn-point high-expressed circRNAs were considered to be highly associated with leaf senescence. Additionally, a total of 17 senescence-associated circRNAs were predicted to have parental genes, in which, regulations of three circRNAs to their parental genes were validated by qRT-PCR. The competing endogenous RNA (ceRNA) networks were also constructed. And a total of 11 senescence-associated circRNAs were predicted to act as miRNA sponges to regulate mRNAs, in which, regulation of two circRNAs to eight mRNAs was validated by qRT-PCR. It is discussed that senescence-associated circRNAs were involved in flag leaf senescence probably through mediating their parental genes and ceRNA networks, to participate in several well-studied senescence-associated processes, mainly including the processes of transcription, translation, and posttranslational modification (especially protein glycosylation), oxidation–reduction process, involvement of senescence-associated genes, hormone signaling pathway, proteolysis, and DNA damage repair. This study not only showed the systematic identification of circRNAs involved in leaf senescence of rice, but also laid a foundation for functional research on candidate circRNAs.